You are hereBiblio / An extended sampling of the configurational space of HPr from E. coli

An extended sampling of the configurational space of HPr from E. coli

Publication Type:

Journal Article

Authors:

de Groot,B.L.; Amadei,A.; Scheek,R.M.; van Nuland,N.A.; Berendsen,H.J.

Source:

Volume 26, Issue 3, p.314 - 322 (1996)

URL:

PM:8953652

Keywords:

Bacterial Proteins; chemistry; Computer Simulation; Escherichia coli; Magnetic Resonance Spectroscopy; Models; Molecular; Phosphoenolpyruvate Sugar Phosphotransferase System; Protein Conformation; Protein Structure; Secondary; Reproducibility of Results

Abstract:

Recently, we developed a method (Amadei et al., J. Biomol. Str. Dyn. 13: 615-626; de Groot et al., J. Biomol. Str. Dyn. 13: 741-751, 1996) to obtain an extended sampling of the configurational space of proteins, using an adapted form of molecular dynamics (MD) simulations, based on the essential dynamics (ED) (Amadei et al., Proteins 17:412-425, 1993) method. In the present study, this ED sampling technique is applied to the histidine-containing phosphocarrier protein HPr from Escherichia coli. We find a cluster of conformations that is an order of magnitude larger than that found for a usual MD simulation of comparable length. The structures in this cluster are geometrically and energetically comparable to NMR structures. Moreover, on average, this large cluster satisfies nearly all NMR-derived distance restraints

Notes:

DA - 19970313
IS - 0887-3585 (Print)
LA - eng
PT - Comparative Study
PT - Journal Article
RN - 0 (Bacterial Proteins)
RN - EC 2.7.1.- (Phosphoenolpyruvate Sugar Phosphotransferase System)
RN - EC 2.7.1.- (phosphocarrier protein HPr)
SB - IM